Feat fast gmt2mat - #506
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Fix failing annotation for uniprots for non primates
reactome.org's live SVG exporter is now behind Cloudflare and returns 403 to server-side requests. Route R-HSA ids through the local SBGN renderer instead: fix getReactomeSVG.SBGN (filename mapping + broken returns) so it renders the bundled .sbgn files and returns a path/NULL, and point getPathwayImage at it. getReactomeSVG now returns NULL on failed download. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Switch Reactome diagrams from SBGNview (which re-renders in generic SBGN style, not matching reactome.org) to Reactome's own native SVGs. Since the live exporter is Cloudflare-blocked, fetch them from a self-hosted mirror (REACTOME_SVG_URL) on demand and cache on disk. Sub-pathways with no diagram of their own resolve to the nearest ancestor diagram via a precomputed offline map (inst/extdata/reactome_diagram_map.tsv), so no reactome.org call is made at runtime. getReactomeSVG.SBGN and the bundled inst/sbgn files are now unused. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The map was keyed off humanPathwaysWithDiagrams.txt (1137), but the SVG tarball ships 1382 diagrams, so common pathways like R-HSA-109581 had a diagram but no map entry and showed "not available". Rebuild the map with the diagram set = ids that actually have an SVG, so every target is guaranteed a file. Coverage goes from 91% (2647) to 100% (2883). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
getReactomeSVG now prefers the gzipped native SVGs bundled in playdata (inst/extdata/reactome-svg), decompressing on demand to the on-disk cache via fast raw-byte streaming, and falls back to the hosted mirror (REACTOME_SVG_URL) when playdata doesn't ship them. The diagram map is likewise read from playdata, falling back to playbase's own copy during the transition. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Drop the transition fallbacks per single-source design: the diagram map is read solely from playdata (playbase's copy removed), and getReactomeSVG serves only the gzipped SVGs bundled in playdata -- the hosted-mirror path (REACTOME_SVG_URL) and its baseurl arg are gone. Deployment guarantees playdata is up to date. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Completes the single-source refactor whose code change was accidentally left out of the previous commit (which only removed the map file). getReactomeSVG now serves solely from playdata's gzipped SVGs (no baseurl / REACTOME_SVG_URL), reactomeDiagramMap reads only playdata, and the roxygen docs + NAMESPACE are regenerated to match. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
We ended up serving native SVGs, so the SBGN renderer is unused. Undo the modifications made to it during the abandoned SBGN approach; leave the (dormant) function otherwise untouched. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
feat: order samples on heatmap
Reactome diagrams: native SVGs via playdata + offline map
A client reported UniProt ranking failed when IDs had a space after the
semicolon: "I3L1P8;Q02978" worked but "I3L1P8; Q02978" did not.
Root cause: the split tokens were never actually trimmed - trimws() was
only used as a filter predicate, not applied to the values. A leading
space made the Swiss-Prot test grep("^[OPQ][0-9]", ...) miss (the ^
anchor hit the space), demoting Swiss-Prot IDs to TrEMBL, and the stray
space leaked into the output feature string.
Fix: trim the tokens themselves. Handles one or multiple spaces and
padding anywhere. Adds a regression test.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Replace with faster implementation of PR from plaid bigomics/plaid#13